Summary stats

General stats about the patient cohort

Stat Value
Unique HPO terms 24
Cohort size 3971
Rejected patients by empty profile 0
HPOs per patient (average) 2.7107
HPO terms per patient: percentile 90 1
Percentage of HPO with more specific children 81.7168
DsI for uniq HP terms 0
DsI for frequency weigthed HP terms 0
Number of unknown phenotypes 0
Number of clusters with mutations accross > 1 chromosomes 2891
Average variant size 4210308.4241
Nucleotides affected by mutations 1728337900
Number of genome windows 1597
Mean patients per genome window 3.9818
Number of genome window shared by >= 2 patients 1097
Number of patients with at least 1 SOR 1027
Nucleotides affected by mutations 974263470

HPO stats

HPOs more frequent in the cohort

HPO Patient percentage
Cognitive impairment 80.96197431377486
Intellectual disability, mild 17.678166708637622
Short stature 17.325610677411234
Autistic behavior 16.872324351548727
Hypotonia 15.361369932007051
Intellectual disability, severe 15.26063963737094
Seizure 15.23545706371191
Behavioral abnormality 13.220851170989675
Microcephaly 12.465373961218837
Intellectual disability, moderate 11.004784688995215
Morphological central nervous system abnormality 8.562075044069504
Intrauterine growth retardation 8.335431881138252
Abnormal external genitalia 6.698564593301436
Attention deficit hyperactivity disorder 5.615713925963233
Macrocephaly 4.960967010828507
Abnormal cardiac septum morphology 4.230672374716696
Abnormality of the upper urinary tract 3.9032989171493324
Conotruncal defect 3.2485520020146064
Tall stature 2.719717955175019
Abnormality of cardiovascular system morphology 2.3419793502896
Abnormal heart valve morphology 2.316796776630572
Abnormality of the lower urinary tract 2.039788466381264
Abnormal internal genitalia 0.4281037522034752
Abnormality of the genitourinary system 0.2770083102493075

Cohort genome coverage analysis

Distribution of the genome coverage of all mutations characterized in the cohort. Second figure shows the same results for SORs.

Distribution of mutations

Distribution of all mutations along the genome (Length) and the number of patients that have at least one of them (Count). Second figure shows the same for SORs.

HPO annotations distribution

Analysis of the HPO terms within the HPO ontology and the cohort of patients. Left: distribution of terms within the ontology and the cohort. Right: percentage of terms distribution within the ontology and the cohort.

HPOs frequency distribution. Colour based on the HPO frequency.

Clustering patients by HPO profile

All patients are clustered using their HPO profiles. First figure shows the information coefficient distribution for the top clusters. Second figure shows which chromosomes are affected in the patients for each top cluster.

HPO profile redundancy

For each patient profile size (number of phenotypes, x-axis) it is shown the number of HPO phenotypes that are parent of other terms within the profile (number of parent terms, y-axis).

HPO ICs distribution

First figure shows the ICs distribution in terms of the HP ontology (x-axis) and for each single HPO term, its frequency in the cohort according to the HP ontology structure (y-axis) and the second figure shows the same distributions considering the profiles analyzed.

HPO frequency by cluster

Patients in Cluster 0 Phenotypes Frequency
688 Cognitive impairment 100.0
Patients in Cluster 1 Phenotypes Frequency
137 Cognitive impairment, Intellectual disability, mild 100.0, 100.0
Patients in Cluster 2 Phenotypes Frequency
106 Cognitive impairment, Autistic behavior 100.0, 100.0
Patients in Cluster 3 Phenotypes Frequency
80 Cognitive impairment, Behavioral abnormality 100.0, 100.0
Patients in Cluster 4 Phenotypes Frequency
71 Cognitive impairment, Intellectual disability, moderate 100.0, 100.0
Patients in Cluster 5 Phenotypes Frequency
66 Cognitive impairment, Intellectual disability, mild, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 6 Phenotypes Frequency
63 Cognitive impairment, Intellectual disability, mild, Behavioral abnormality, Abnormal cardiac septum morphology, Abnormality of the genitourinary system 100.0, 100.0, 100.0, 1.5873, 1.5873
Patients in Cluster 7 Phenotypes Frequency
62 Short stature 100.0
Patients in Cluster 8 Phenotypes Frequency
60 Cognitive impairment, Seizure 100.0, 100.0
Patients in Cluster 9 Phenotypes Frequency
48 Behavioral abnormality 100.0
Patients in Cluster 10 Phenotypes Frequency
47 Cognitive impairment, Short stature 100.0, 100.0
Patients in Cluster 11 Phenotypes Frequency
47 Cognitive impairment, Intellectual disability, severe 100.0, 100.0
Patients in Cluster 12 Phenotypes Frequency
45 Cognitive impairment, Hypotonia 100.0, 100.0
Patients in Cluster 13 Phenotypes Frequency
41 Cognitive impairment, Intellectual disability, moderate, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 14 Phenotypes Frequency
40 Autistic behavior 100.0
Patients in Cluster 15 Phenotypes Frequency
39 Cognitive impairment, Intellectual disability, severe, Autistic behavior 100.0, 100.0, 100.0
Patients in Cluster 16 Phenotypes Frequency
38 Morphological central nervous system abnormality 100.0
Patients in Cluster 17 Phenotypes Frequency
38 Abnormality of cardiovascular system morphology, Behavioral abnormality 100.0, 2.6316
Patients in Cluster 18 Phenotypes Frequency
33 Hypotonia 100.0
Patients in Cluster 19 Phenotypes Frequency
31 Abnormality of the upper urinary tract 100.0
Patients in Cluster 20 Phenotypes Frequency
30 Cognitive impairment, Intellectual disability, mild, Short stature 100.0, 100.0, 100.0
Patients in Cluster 21 Phenotypes Frequency
27 Cognitive impairment, Microcephaly 100.0, 100.0
Patients in Cluster 22 Phenotypes Frequency
26 Cognitive impairment, Intellectual disability, severe, Seizure, Abnormal internal genitalia, Abnormal cardiac septum morphology 100.0, 100.0, 100.0, 3.8462, 3.8462
Patients in Cluster 23 Phenotypes Frequency
25 Microcephaly 100.0
Patients in Cluster 24 Phenotypes Frequency
25 Cognitive impairment, Intellectual disability, severe, Behavioral abnormality, Abnormal internal genitalia 100.0, 100.0, 100.0, 4.0

Patient profiles heatmaps

For each patient, their HPO profile similarity coefficient is calculated according to the different methods specified in the analysis and represented in these heatmaps.